Filtered
#Calculate Hill numbers
richness <- genome_counts_filt %>%
column_to_rownames(var="genome") %>%
select(where(~!all(. == 0))) %>%
hilldiv(.,q=0) %>%
t() %>%
as.data.frame() %>%
rename(richness=1) %>%
rownames_to_column(var="microsample")
neutral <- genome_counts_filt %>%
column_to_rownames(var="genome") %>%
select(where(~!all(. == 0))) %>%
hilldiv(.,q=1) %>%
t() %>%
as.data.frame() %>%
rename(neutral=1) %>%
rownames_to_column(var="microsample")
phylogenetic <- genome_counts_filt %>%
column_to_rownames(var="genome") %>%
select(where(~!all(. == 0))) %>%
hilldiv(.,q=1,tree=genome_tree) %>%
t() %>%
as.data.frame() %>%
rename(phylogenetic=1) %>%
rownames_to_column(var="microsample")
# Merge alpha diversities
alpha_diversity <- richness %>%
full_join(neutral,by=join_by(microsample==microsample)) %>%
full_join(phylogenetic,by=join_by(microsample==microsample)) %>%
left_join(sample_metadata, by=join_by(microsample==microsample))
# Write alpha diversities
alpha_diversity %>% write_tsv("results/alpha_div_filtered.tsv")
# Print alpha diversity
alpha_diversity %>%
select(microsample,richness, neutral, phylogenetic, section, buffer, batch, Xcoord, Ycoord, size) %>%
tt()
tinytable_8x9sj8eztwd1brqj29x0
| microsample |
richness |
neutral |
phylogenetic |
section |
buffer |
batch |
Xcoord |
Ycoord |
size |
| M300554 |
105 |
45.801912 |
3.937760 |
Caecum right |
B11 |
MSEB0006 |
74953.33 |
27445.67 |
4976 |
| M300555 |
3 |
2.654441 |
1.663073 |
Caecum right |
B11 |
MSEB0006 |
72020.28 |
33695.14 |
4976 |
| M300556 |
3 |
2.921247 |
1.820079 |
Caecum right |
B11 |
MSEB0006 |
75415.39 |
27819.35 |
4976 |
| M300557 |
81 |
43.169579 |
3.736918 |
Caecum right |
B11 |
MSEB0006 |
76113.48 |
28351.85 |
4976 |
| M300559 |
105 |
46.235275 |
3.950650 |
Caecum right |
B11 |
MSEB0006 |
76849.23 |
29025.05 |
4976 |
| M300560 |
99 |
44.437305 |
4.093363 |
Caecum right |
B11 |
MSEB0006 |
75971.70 |
29352.86 |
4976 |
| M300561 |
103 |
44.311493 |
4.120349 |
Caecum right |
B11 |
MSEB0006 |
76680.94 |
29558.16 |
4976 |
| M300562 |
103 |
46.882732 |
4.048584 |
Caecum right |
B11 |
MSEB0006 |
74883.32 |
29170.18 |
5140 |
| M300563 |
109 |
47.059960 |
4.017112 |
Caecum right |
B11 |
MSEB0006 |
75220.99 |
29120.51 |
5140 |
| M300564 |
12 |
10.477468 |
2.973998 |
Caecum right |
B11 |
MSEB0006 |
75894.62 |
29134.86 |
5140 |
| M300566 |
93 |
43.059847 |
3.786416 |
Caecum right |
B11 |
MSEB0006 |
76922.54 |
29224.45 |
5140 |
| M300567 |
99 |
44.029116 |
4.039769 |
Caecum right |
B11 |
MSEB0006 |
77492.20 |
29097.78 |
5140 |
| M300569 |
100 |
46.805777 |
4.129635 |
Caecum right |
B11 |
MSEB0006 |
77495.46 |
28977.76 |
5140 |
| M300570 |
100 |
44.462204 |
3.978752 |
Caecum right |
B11 |
MSEB0006 |
74950.84 |
28473.11 |
4815 |
| M300571 |
94 |
42.482781 |
3.903377 |
Caecum right |
B11 |
MSEB0006 |
75619.95 |
28632.40 |
4815 |
| M300572 |
56 |
32.680577 |
3.764339 |
Caecum right |
B11 |
MSEB0006 |
76345.93 |
29031.81 |
4815 |
| M300574 |
97 |
43.914978 |
3.991990 |
Caecum right |
B11 |
MSEB0006 |
76921.00 |
29347.99 |
4815 |
| M300576 |
92 |
43.158898 |
3.979982 |
Caecum right |
B11 |
MSEB0006 |
77104.53 |
29588.79 |
4815 |
| M300577 |
103 |
44.666492 |
4.003275 |
Caecum right |
B11 |
MSEB0006 |
77418.90 |
29907.92 |
4815 |
| M300578 |
101 |
44.526067 |
3.942073 |
Caecum right |
B12 |
MSEB0006 |
76897.21 |
30198.48 |
5140 |
| M300580 |
102 |
43.777961 |
3.966526 |
Caecum right |
B12 |
MSEB0006 |
77026.94 |
30039.53 |
5140 |
| M300581 |
79 |
39.975639 |
3.898216 |
Caecum right |
B12 |
MSEB0006 |
77028.60 |
29718.20 |
5140 |
| M300582 |
78 |
38.898531 |
3.907879 |
Caecum right |
B12 |
MSEB0006 |
77019.21 |
29448.24 |
5140 |
| M300583 |
95 |
38.373844 |
4.002493 |
Caecum right |
B12 |
MSEB0006 |
77009.20 |
28923.10 |
5140 |
| M300584 |
104 |
44.918626 |
3.992409 |
Caecum right |
B12 |
MSEB0006 |
77019.41 |
28061.84 |
5140 |
| M300588 |
102 |
42.618728 |
3.997889 |
Caecum right |
B12 |
MSEB0006 |
75330.02 |
26890.36 |
5141 |
| M300589 |
99 |
41.459691 |
3.963052 |
Caecum right |
B12 |
MSEB0006 |
75862.87 |
27323.96 |
5141 |
| M300590 |
96 |
40.482162 |
4.131238 |
Caecum right |
B12 |
MSEB0006 |
76508.23 |
27653.84 |
5141 |
| M300592 |
103 |
40.971234 |
4.092363 |
Caecum right |
B12 |
MSEB0006 |
77351.46 |
28017.27 |
5141 |
| M300593 |
98 |
42.126550 |
4.082443 |
Caecum right |
B12 |
MSEB0006 |
77854.22 |
28261.49 |
5141 |
| M300594 |
96 |
43.659879 |
4.066965 |
Caecum right |
B12 |
MSEB0006 |
75509.65 |
26477.82 |
4976 |
| M300595 |
102 |
37.738766 |
4.076473 |
Caecum right |
B12 |
MSEB0006 |
75650.54 |
26591.91 |
4976 |
| M300596 |
105 |
40.160724 |
4.060594 |
Caecum right |
B12 |
MSEB0006 |
75822.84 |
26598.11 |
4976 |
| M300597 |
100 |
40.582505 |
4.107775 |
Caecum right |
B12 |
MSEB0006 |
76147.10 |
26625.28 |
4976 |
| M300598 |
101 |
41.887011 |
4.052863 |
Caecum right |
B12 |
MSEB0006 |
76899.24 |
26623.52 |
4976 |
| M300599 |
104 |
42.932100 |
3.970582 |
Caecum right |
B12 |
MSEB0006 |
76852.73 |
26643.02 |
4976 |
| M300602 |
4 |
3.258694 |
1.449831 |
Ileum |
B11 |
MSEB0006 |
104424.70 |
42749.48 |
5140 |
| M300603 |
3 |
2.026603 |
1.266765 |
Ileum |
B11 |
MSEB0006 |
104606.90 |
42459.54 |
5140 |
| M300605 |
2 |
1.729081 |
1.216363 |
Ileum |
B11 |
MSEB0006 |
104954.50 |
42730.89 |
5140 |
| M300606 |
1 |
1.000000 |
1.000000 |
Ileum |
B11 |
MSEB0006 |
105122.50 |
42666.74 |
5140 |
| M300608 |
4 |
2.614424 |
1.430317 |
Ileum |
B11 |
MSEB0006 |
105262.70 |
42589.77 |
5140 |
| M300609 |
4 |
3.096111 |
1.458992 |
Ileum |
B11 |
MSEB0006 |
105328.90 |
42703.60 |
5140 |
| M300610 |
4 |
3.092445 |
1.481998 |
Ileum |
B11 |
MSEB0006 |
105102.40 |
41497.10 |
4976 |
| M300611 |
1 |
1.000000 |
1.000000 |
Ileum |
B11 |
MSEB0006 |
105146.00 |
41596.22 |
4976 |
| M300612 |
4 |
3.200070 |
1.470375 |
Ileum |
B11 |
MSEB0006 |
105281.00 |
41702.52 |
4976 |
| M300613 |
1 |
1.000000 |
1.000000 |
Ileum |
B11 |
MSEB0006 |
105408.30 |
41533.66 |
4976 |
| M300616 |
3 |
1.602470 |
1.194510 |
Ileum |
B11 |
MSEB0006 |
105595.70 |
41999.37 |
4976 |
| M300617 |
4 |
2.597621 |
1.413674 |
Ileum |
B11 |
MSEB0006 |
105983.00 |
42106.21 |
4976 |
| M300619 |
3 |
1.859573 |
1.239761 |
Ileum |
B11 |
MSEB0006 |
106845.70 |
41525.80 |
5306 |
| M300622 |
3 |
2.658765 |
1.355956 |
Ileum |
B11 |
MSEB0006 |
107262.30 |
42133.87 |
5306 |
| M300623 |
3 |
2.873136 |
1.383011 |
Ileum |
B11 |
MSEB0006 |
107820.60 |
41925.02 |
5306 |
| M300624 |
1 |
1.000000 |
1.000000 |
Ileum |
B11 |
MSEB0006 |
107233.50 |
41764.35 |
5306 |
| M300627 |
3 |
2.862931 |
1.381746 |
Ileum |
B12 |
MSEB0006 |
108112.00 |
45420.81 |
4815 |
| M300628 |
4 |
2.628829 |
1.503377 |
Ileum |
B12 |
MSEB0006 |
108221.60 |
45346.45 |
4815 |
| M300629 |
4 |
1.907144 |
1.304654 |
Ileum |
B12 |
MSEB0006 |
108085.50 |
45636.13 |
4815 |
| M300630 |
4 |
1.854313 |
1.283251 |
Ileum |
B12 |
MSEB0006 |
108093.70 |
45848.93 |
4815 |
| M300631 |
5 |
3.608828 |
1.726759 |
Ileum |
B12 |
MSEB0006 |
107697.50 |
45704.29 |
4815 |
| M300633 |
6 |
2.179216 |
1.436402 |
Ileum |
B12 |
MSEB0006 |
107727.50 |
45487.09 |
4815 |
| M300634 |
5 |
2.654260 |
1.436436 |
Ileum |
B12 |
MSEB0006 |
106635.90 |
42106.55 |
5384 |
| M300636 |
4 |
2.513021 |
1.488272 |
Ileum |
B12 |
MSEB0006 |
106545.50 |
42220.70 |
5384 |
| M300638 |
4 |
2.712719 |
1.467680 |
Ileum |
B12 |
MSEB0006 |
106647.00 |
42288.86 |
5384 |
| M300639 |
7 |
2.562594 |
1.490282 |
Ileum |
B12 |
MSEB0006 |
106800.50 |
41821.88 |
5384 |
| M300640 |
3 |
2.025162 |
1.266492 |
Ileum |
B12 |
MSEB0006 |
107052.70 |
42525.49 |
5384 |
| M300642 |
1 |
1.000000 |
1.000000 |
Ileum |
B12 |
MSEB0006 |
108030.70 |
43599.50 |
4976 |
| M300644 |
5 |
1.600004 |
1.210094 |
Ileum |
B12 |
MSEB0006 |
NA |
NA |
NA |
| M300645 |
5 |
1.502894 |
1.241772 |
Ileum |
B12 |
MSEB0006 |
107988.20 |
43509.47 |
4976 |
| M300647 |
5 |
3.154388 |
1.460507 |
Ileum |
B12 |
MSEB0006 |
107969.50 |
43138.84 |
4976 |
| M300648 |
5 |
1.758864 |
1.268011 |
Ileum |
B12 |
MSEB0006 |
107883.70 |
43169.50 |
4976 |
| M300704 |
47 |
26.137840 |
3.656487 |
Colon |
B11 |
MSEB0010 |
10676.97 |
15665.82 |
5140 |
| M300705 |
62 |
39.308166 |
3.660768 |
Colon |
B11 |
MSEB0010 |
10812.32 |
15756.81 |
5140 |
| M300706 |
58 |
33.851408 |
3.774257 |
Colon |
B11 |
MSEB0010 |
11055.42 |
15656.04 |
5140 |
| M300707 |
74 |
38.632295 |
3.920088 |
Colon |
B11 |
MSEB0010 |
11216.84 |
15649.19 |
5140 |
| M300708 |
85 |
41.477440 |
3.830608 |
Colon |
B11 |
MSEB0010 |
11879.87 |
15812.03 |
5140 |
| M300711 |
83 |
40.402932 |
3.871549 |
Colon |
B11 |
MSEB0010 |
12278.13 |
15716.47 |
5140 |
| M300712 |
84 |
42.428071 |
3.859852 |
Colon |
B11 |
MSEB0010 |
12139.94 |
15889.85 |
4976 |
| M300714 |
77 |
39.203234 |
3.974200 |
Colon |
B11 |
MSEB0010 |
12138.96 |
16135.22 |
4976 |
| M300715 |
84 |
41.934901 |
3.820654 |
Colon |
B11 |
MSEB0010 |
12164.85 |
16944.14 |
4976 |
| M300716 |
64 |
38.066001 |
3.624855 |
Colon |
B11 |
MSEB0010 |
12650.44 |
17948.63 |
4976 |
| M300717 |
66 |
38.461828 |
3.862272 |
Colon |
B11 |
MSEB0010 |
13434.73 |
19286.92 |
4976 |
| M300718 |
96 |
46.399944 |
3.883736 |
Colon |
B11 |
MSEB0010 |
13238.20 |
20246.16 |
4976 |
| M300721 |
92 |
47.317073 |
3.759318 |
Colon |
B11 |
MSEB0010 |
10372.82 |
20398.48 |
5306 |
| M300722 |
56 |
33.260330 |
3.727113 |
Colon |
B11 |
MSEB0010 |
11173.11 |
20408.59 |
5306 |
| M300724 |
80 |
43.719402 |
3.794995 |
Colon |
B11 |
MSEB0010 |
13295.25 |
18310.97 |
5306 |
| M300725 |
21 |
17.447617 |
2.930725 |
Colon |
B11 |
MSEB0010 |
12939.03 |
18128.54 |
5306 |
| M300727 |
81 |
41.998480 |
3.947856 |
Colon |
B11 |
MSEB0010 |
12777.09 |
17606.38 |
5306 |
| M300729 |
8 |
7.637585 |
2.619316 |
Colon |
B11 |
MSEB0010 |
12551.79 |
21653.42 |
4815 |
| M300730 |
14 |
12.494169 |
2.806653 |
Colon |
B11 |
MSEB0010 |
12478.73 |
21318.48 |
4815 |
| M300731 |
78 |
42.804279 |
3.541318 |
Colon |
B11 |
MSEB0010 |
12362.88 |
20562.75 |
4815 |
| M300733 |
29 |
21.650469 |
3.174838 |
Colon |
B11 |
MSEB0010 |
12653.67 |
19720.44 |
4815 |
| M300735 |
67 |
39.697104 |
3.650732 |
Colon |
B11 |
MSEB0010 |
11471.31 |
19136.40 |
4815 |
| M300736 |
89 |
44.552604 |
3.826006 |
Colon |
B11 |
MSEB0010 |
13507.34 |
18129.93 |
5647 |
| M300738 |
85 |
45.260227 |
3.746172 |
Colon |
B11 |
MSEB0010 |
13010.06 |
17942.33 |
5647 |
| M300741 |
75 |
40.579742 |
3.741690 |
Colon |
B11 |
MSEB0010 |
12684.37 |
17716.75 |
5647 |
| M300742 |
82 |
42.384536 |
3.881068 |
Colon |
B11 |
MSEB0010 |
12621.55 |
17543.54 |
5647 |
| M300743 |
76 |
41.817272 |
3.730852 |
Colon |
B11 |
MSEB0010 |
12372.90 |
16657.60 |
5647 |
| M300744 |
32 |
24.141380 |
3.136654 |
Colon |
B11 |
MSEB0010 |
11994.45 |
14153.13 |
4976 |
| M300745 |
59 |
36.354256 |
3.462527 |
Colon |
B11 |
MSEB0010 |
12007.50 |
14299.24 |
4976 |
| M300747 |
85 |
45.968277 |
3.649012 |
Colon |
B11 |
MSEB0010 |
12029.35 |
14662.48 |
4976 |
| M300748 |
64 |
37.120180 |
3.504468 |
Colon |
B11 |
MSEB0010 |
12076.59 |
15671.87 |
4976 |
| M300750 |
73 |
39.843866 |
3.738390 |
Colon |
B11 |
MSEB0010 |
12060.51 |
16688.98 |
4976 |
| M300751 |
80 |
43.869573 |
3.738696 |
Colon |
B11 |
MSEB0010 |
11931.20 |
19713.77 |
4976 |
| M300753 |
65 |
35.118403 |
3.589983 |
Colon |
B12 |
MSEB0010 |
13884.30 |
20066.13 |
4815 |
| M300755 |
76 |
38.643425 |
3.896215 |
Colon |
B12 |
MSEB0010 |
13715.68 |
19528.97 |
4815 |
| M300756 |
103 |
43.201393 |
3.990432 |
Colon |
B12 |
MSEB0010 |
13508.64 |
19087.25 |
4815 |
| M300757 |
83 |
39.509499 |
3.977505 |
Colon |
B12 |
MSEB0010 |
13209.32 |
18911.46 |
4815 |
| M300758 |
98 |
47.502632 |
3.784666 |
Colon |
B12 |
MSEB0010 |
13454.50 |
18211.88 |
4815 |
| M300759 |
105 |
45.507585 |
4.065463 |
Colon |
B12 |
MSEB0010 |
13356.63 |
17525.29 |
4815 |
| M300760 |
78 |
37.482344 |
3.895542 |
Colon |
B12 |
MSEB0010 |
12866.49 |
15050.07 |
5140 |
| M300761 |
115 |
45.578238 |
4.024987 |
Colon |
B12 |
MSEB0010 |
12921.94 |
15311.99 |
5140 |
| M300763 |
125 |
50.960537 |
3.971121 |
Colon |
B12 |
MSEB0010 |
12995.95 |
15577.55 |
5140 |
| M300764 |
115 |
48.329755 |
3.842227 |
Colon |
B12 |
MSEB0010 |
12999.11 |
16205.10 |
5140 |
| M300766 |
112 |
46.704807 |
4.063781 |
Colon |
B12 |
MSEB0010 |
13128.60 |
18741.54 |
5140 |
| M300767 |
100 |
41.243887 |
3.894222 |
Colon |
B12 |
MSEB0010 |
13103.68 |
20085.08 |
5140 |
| M300768 |
79 |
38.784598 |
3.840394 |
Colon |
B12 |
MSEB0010 |
12299.78 |
15261.25 |
4815 |
| M300771 |
58 |
34.643272 |
3.720942 |
Colon |
B12 |
MSEB0010 |
12230.64 |
14216.24 |
4815 |
| M300772 |
102 |
47.639783 |
3.790707 |
Colon |
B12 |
MSEB0010 |
12192.80 |
14393.52 |
4815 |
| M300773 |
106 |
50.262746 |
3.545739 |
Colon |
B12 |
MSEB0010 |
12122.68 |
16011.33 |
4815 |
| M300774 |
114 |
46.306826 |
4.058256 |
Colon |
B12 |
MSEB0010 |
12155.62 |
16716.47 |
4815 |
| M300775 |
92 |
40.482612 |
3.917541 |
Colon |
B12 |
MSEB0010 |
12941.43 |
17792.21 |
4815 |
| M300776 |
71 |
37.655019 |
3.747935 |
Colon |
B12 |
MSEB0010 |
10481.87 |
16446.70 |
5306 |
| M300778 |
82 |
41.038918 |
3.831210 |
Colon |
B12 |
MSEB0010 |
10349.88 |
16974.87 |
5306 |
| M300780 |
88 |
40.130094 |
3.880301 |
Colon |
B12 |
MSEB0010 |
10386.11 |
17635.79 |
5306 |
| M300782 |
86 |
39.302414 |
3.892170 |
Colon |
B12 |
MSEB0010 |
10499.61 |
18348.85 |
5306 |
| M300783 |
67 |
37.371632 |
3.772192 |
Colon |
B12 |
MSEB0010 |
10505.18 |
19231.33 |
5306 |
| M300784 |
63 |
33.764525 |
3.734824 |
Colon |
B12 |
MSEB0010 |
11637.20 |
19482.30 |
4656 |
| M300786 |
44 |
28.493828 |
3.612460 |
Colon |
B12 |
MSEB0010 |
11099.18 |
18995.87 |
4656 |
| M300787 |
106 |
45.535131 |
3.977904 |
Colon |
B12 |
MSEB0010 |
10460.97 |
19686.94 |
4656 |
| M300788 |
62 |
33.583894 |
3.720720 |
Colon |
B12 |
MSEB0010 |
10442.08 |
20914.36 |
4656 |
| M300791 |
47 |
26.239698 |
3.687149 |
Colon |
B12 |
MSEB0010 |
11146.56 |
21763.22 |
4656 |
| M300792 |
103 |
44.068606 |
4.152050 |
Colon |
B12 |
MSEB0010 |
11630.33 |
20543.59 |
5140 |
| M300794 |
105 |
44.712540 |
3.957158 |
Colon |
B12 |
MSEB0010 |
11673.94 |
21223.36 |
5140 |
| M300797 |
96 |
39.849925 |
3.926466 |
Colon |
B12 |
MSEB0010 |
12879.98 |
20904.88 |
5140 |
| M300798 |
116 |
39.422201 |
4.074559 |
Colon |
B12 |
MSEB0010 |
12256.49 |
21371.45 |
5140 |
# Print alpha diversity summary
alpha_diversity %>%
select(richness, neutral, phylogenetic, section, batch) %>%
group_by(section, batch) %>%
summarise(richness=mean(richness), neutral=mean(neutral), phylogenetic=mean(phylogenetic)) %>%
tt()
tinytable_qfacpcfg64x0i8t7yu7n
| section |
batch |
richness |
neutral |
phylogenetic |
| Caecum right |
MSEB0006 |
89.50000 |
39.563947 |
3.840313 |
| Colon |
MSEB0010 |
77.96923 |
38.850665 |
3.748993 |
| Ileum |
MSEB0006 |
3.59375 |
2.222942 |
1.322728 |
alpha_diversity %>%
pivot_longer(!c(microsample,section,cryosection,type,buffer,batch,Xcoord,Ycoord,size), names_to = "metric", values_to = "value") %>%
left_join(quality,by=join_by(microsample==microsample)) %>%
mutate(metric=factor(metric,levels=c("richness","neutral","phylogenetic"))) %>%
ggplot(aes(x=section, y=value, color=quality, group=section))+
scale_color_gradient(low = "red", high = "green", name = "Quality") +
geom_boxplot(outlier.shape = NA) +
geom_jitter(width=0.2) +
facet_grid(metric ~ section, scales = "free")

Unfiltered
#Calculate Hill numbers
richness <- genome_counts %>%
column_to_rownames(var="genome") %>%
select(where(~!all(. == 0))) %>%
hilldiv(.,q=0) %>%
t() %>%
as.data.frame() %>%
rename(richness=1) %>%
rownames_to_column(var="microsample")
neutral <- genome_counts %>%
column_to_rownames(var="genome") %>%
select(where(~!all(. == 0))) %>%
hilldiv(.,q=1) %>%
t() %>%
as.data.frame() %>%
rename(neutral=1) %>%
rownames_to_column(var="microsample")
phylogenetic <- genome_counts %>%
column_to_rownames(var="genome") %>%
select(where(~!all(. == 0))) %>%
hilldiv(.,q=1,tree=genome_tree) %>%
t() %>%
as.data.frame() %>%
rename(phylogenetic=1) %>%
rownames_to_column(var="microsample")
# Merge alpha diversities
alpha_diversity <- richness %>%
full_join(neutral,by=join_by(microsample==microsample)) %>%
full_join(phylogenetic,by=join_by(microsample==microsample)) %>%
left_join(sample_metadata, by=join_by(microsample==microsample))
# Write alpha diversities
alpha_diversity %>% write_tsv("results/alpha_div_unfiltered.tsv")
# Print alpha diversity
alpha_diversity %>%
select(microsample,richness, neutral, phylogenetic, section, buffer, Xcoord, Ycoord, size) %>%
tt()
tinytable_srakodzdy7yerla62pth
| microsample |
richness |
neutral |
phylogenetic |
section |
buffer |
Xcoord |
Ycoord |
size |
| M300554 |
252 |
59.048724 |
4.005426 |
Caecum right |
B11 |
74953.325 |
27445.67 |
4976 |
| M300555 |
234 |
29.591689 |
3.136402 |
Caecum right |
B11 |
72020.280 |
33695.14 |
4976 |
| M300556 |
242 |
52.377341 |
3.862228 |
Caecum right |
B11 |
75415.387 |
27819.35 |
4976 |
| M300557 |
252 |
60.880377 |
3.919625 |
Caecum right |
B11 |
76113.477 |
28351.85 |
4976 |
| M300558 |
147 |
16.388623 |
3.084364 |
Caecum right |
B11 |
NA |
NA |
NA |
| M300559 |
252 |
59.602278 |
4.019172 |
Caecum right |
B11 |
76849.228 |
29025.05 |
4976 |
| M300560 |
252 |
58.645287 |
4.181971 |
Caecum right |
B11 |
75971.705 |
29352.86 |
4976 |
| M300561 |
252 |
57.105278 |
4.190661 |
Caecum right |
B11 |
76680.937 |
29558.16 |
4976 |
| M300562 |
252 |
60.378741 |
4.115130 |
Caecum right |
B11 |
74883.318 |
29170.18 |
5140 |
| M300563 |
252 |
59.645294 |
4.072592 |
Caecum right |
B11 |
75220.992 |
29120.51 |
5140 |
| M300564 |
246 |
52.890970 |
4.203353 |
Caecum right |
B11 |
75894.617 |
29134.86 |
5140 |
| M300565 |
48 |
13.113524 |
4.215440 |
Caecum right |
B11 |
72986.812 |
36482.20 |
5140 |
| M300566 |
251 |
58.164898 |
3.882696 |
Caecum right |
B11 |
76922.541 |
29224.45 |
5140 |
| M300567 |
252 |
57.810869 |
4.124295 |
Caecum right |
B11 |
77492.203 |
29097.78 |
5140 |
| M300568 |
40 |
10.638020 |
2.635867 |
Caecum right |
B11 |
NA |
NA |
NA |
| M300569 |
252 |
60.745119 |
4.196834 |
Caecum right |
B11 |
77495.465 |
28977.76 |
5140 |
| M300570 |
252 |
57.723816 |
4.052962 |
Caecum right |
B11 |
74950.841 |
28473.11 |
4815 |
| M300571 |
251 |
56.661744 |
4.017740 |
Caecum right |
B11 |
75619.946 |
28632.40 |
4815 |
| M300572 |
249 |
56.949762 |
4.191364 |
Caecum right |
B11 |
76345.933 |
29031.81 |
4815 |
| M300573 |
178 |
34.564442 |
3.598634 |
Caecum right |
B11 |
74609.411 |
34469.39 |
4815 |
| M300574 |
251 |
57.725467 |
4.082745 |
Caecum right |
B11 |
76920.997 |
29347.99 |
4815 |
| M300575 |
135 |
59.863456 |
4.655632 |
Caecum right |
B11 |
NA |
NA |
NA |
| M300576 |
251 |
57.389815 |
4.083745 |
Caecum right |
B11 |
77104.532 |
29588.79 |
4815 |
| M300577 |
252 |
57.842513 |
4.079376 |
Caecum right |
B11 |
77418.895 |
29907.92 |
4815 |
| M300578 |
252 |
57.743125 |
4.012410 |
Caecum right |
B12 |
76897.212 |
30198.48 |
5140 |
| M300579 |
221 |
38.829262 |
3.357156 |
Caecum right |
B12 |
73304.285 |
36352.33 |
5140 |
| M300580 |
250 |
55.871239 |
4.042301 |
Caecum right |
B12 |
77026.940 |
30039.53 |
5140 |
| M300581 |
252 |
56.693254 |
4.077549 |
Caecum right |
B12 |
77028.597 |
29718.20 |
5140 |
| M300582 |
251 |
55.908533 |
4.078589 |
Caecum right |
B12 |
77019.213 |
29448.24 |
5140 |
| M300583 |
252 |
51.029088 |
4.100996 |
Caecum right |
B12 |
77009.202 |
28923.10 |
5140 |
| M300584 |
252 |
57.684739 |
4.058398 |
Caecum right |
B12 |
77019.413 |
28061.84 |
5140 |
| M300585 |
85 |
36.312174 |
5.379855 |
Caecum right |
B12 |
NA |
NA |
NA |
| M300586 |
48 |
21.091967 |
4.510739 |
Caecum right |
B12 |
73652.539 |
35857.69 |
5141 |
| M300587 |
8 |
3.491849 |
1.592392 |
Caecum right |
B12 |
NA |
NA |
NA |
| M300588 |
252 |
54.764773 |
4.072549 |
Caecum right |
B12 |
75330.017 |
26890.36 |
5141 |
| M300589 |
253 |
54.565428 |
4.052600 |
Caecum right |
B12 |
75862.866 |
27323.96 |
5141 |
| M300590 |
252 |
53.695112 |
4.232105 |
Caecum right |
B12 |
76508.231 |
27653.84 |
5141 |
| M300591 |
193 |
44.669792 |
3.308027 |
Caecum right |
B12 |
76848.926 |
27815.44 |
5141 |
| M300592 |
251 |
52.703789 |
4.157326 |
Caecum right |
B12 |
77351.464 |
28017.27 |
5141 |
| M300593 |
253 |
54.697582 |
4.159239 |
Caecum right |
B12 |
77854.216 |
28261.49 |
5141 |
| M300594 |
252 |
57.267685 |
4.154592 |
Caecum right |
B12 |
75509.650 |
26477.82 |
4976 |
| M300595 |
251 |
49.303188 |
4.159722 |
Caecum right |
B12 |
75650.540 |
26591.91 |
4976 |
| M300596 |
252 |
51.537550 |
4.129928 |
Caecum right |
B12 |
75822.838 |
26598.11 |
4976 |
| M300597 |
251 |
52.894386 |
4.187497 |
Caecum right |
B12 |
76147.102 |
26625.28 |
4976 |
| M300598 |
252 |
54.366506 |
4.127848 |
Caecum right |
B12 |
76899.245 |
26623.52 |
4976 |
| M300599 |
252 |
55.014439 |
4.041644 |
Caecum right |
B12 |
76852.725 |
26643.02 |
4976 |
| M300600 |
37 |
12.471508 |
3.871589 |
Caecum right |
B12 |
NA |
NA |
NA |
| M300601 |
122 |
44.752920 |
6.549661 |
Caecum right |
B12 |
72982.582 |
21722.53 |
4976 |
| M300602 |
195 |
3.770399 |
1.526286 |
Ileum |
B11 |
104424.700 |
42749.48 |
5140 |
| M300603 |
172 |
3.443781 |
1.761321 |
Ileum |
B11 |
104606.900 |
42459.54 |
5140 |
| M300604 |
54 |
11.488595 |
3.430860 |
Ileum |
B11 |
101758.400 |
36668.70 |
5140 |
| M300605 |
154 |
3.468041 |
1.580848 |
Ileum |
B11 |
104954.500 |
42730.89 |
5140 |
| M300606 |
231 |
42.312840 |
4.055184 |
Ileum |
B11 |
105122.500 |
42666.74 |
5140 |
| M300607 |
25 |
4.742713 |
1.877699 |
Ileum |
B11 |
NA |
NA |
NA |
| M300608 |
180 |
3.093547 |
1.514223 |
Ileum |
B11 |
105262.700 |
42589.77 |
5140 |
| M300609 |
207 |
3.586403 |
1.515176 |
Ileum |
B11 |
105328.900 |
42703.60 |
5140 |
| M300610 |
193 |
3.434464 |
1.521143 |
Ileum |
B11 |
105102.400 |
41497.10 |
4976 |
| M300611 |
75 |
4.120703 |
1.781889 |
Ileum |
B11 |
105146.000 |
41596.22 |
4976 |
| M300612 |
186 |
3.576177 |
1.512044 |
Ileum |
B11 |
105281.000 |
41702.52 |
4976 |
| M300613 |
71 |
2.227148 |
1.360170 |
Ileum |
B11 |
105408.300 |
41533.66 |
4976 |
| M300614 |
51 |
13.957408 |
4.473484 |
Ileum |
B11 |
101928.600 |
37181.60 |
4976 |
| M300615 |
76 |
33.344988 |
4.963147 |
Ileum |
B11 |
NA |
NA |
NA |
| M300616 |
174 |
1.845652 |
1.249203 |
Ileum |
B11 |
105595.700 |
41999.37 |
4976 |
| M300617 |
236 |
5.332503 |
1.984855 |
Ileum |
B11 |
105983.000 |
42106.21 |
4976 |
| M300618 |
56 |
8.503252 |
2.626672 |
Ileum |
B11 |
101861.400 |
37375.71 |
5306 |
| M300619 |
175 |
2.550470 |
1.410755 |
Ileum |
B11 |
106845.700 |
41525.80 |
5306 |
| M300620 |
28 |
7.640770 |
2.905044 |
Ileum |
B11 |
NA |
NA |
NA |
| M300621 |
119 |
12.148781 |
3.349201 |
Ileum |
B11 |
107360.500 |
41744.06 |
5306 |
| M300622 |
221 |
4.591257 |
1.766175 |
Ileum |
B11 |
107262.300 |
42133.87 |
5306 |
| M300623 |
160 |
3.966379 |
1.799967 |
Ileum |
B11 |
107820.600 |
41925.02 |
5306 |
| M300624 |
115 |
1.651694 |
1.232074 |
Ileum |
B11 |
107233.500 |
41764.35 |
5306 |
| M300625 |
144 |
5.388601 |
2.320102 |
Ileum |
B11 |
107258.100 |
42448.02 |
5306 |
| M300626 |
41 |
8.538645 |
2.863586 |
Ileum |
B12 |
NA |
NA |
NA |
| M300627 |
144 |
3.518088 |
1.512361 |
Ileum |
B12 |
108112.000 |
45420.81 |
4815 |
| M300628 |
175 |
3.173885 |
1.607903 |
Ileum |
B12 |
108221.600 |
45346.45 |
4815 |
| M300629 |
182 |
2.393480 |
1.450458 |
Ileum |
B12 |
108085.500 |
45636.13 |
4815 |
| M300630 |
182 |
2.332205 |
1.406259 |
Ileum |
B12 |
108093.700 |
45848.93 |
4815 |
| M300631 |
208 |
4.627633 |
1.966486 |
Ileum |
B12 |
107697.500 |
45704.29 |
4815 |
| M300632 |
139 |
31.364862 |
4.012416 |
Ileum |
B12 |
102872.400 |
38456.93 |
4815 |
| M300633 |
216 |
2.511084 |
1.495177 |
Ileum |
B12 |
107727.500 |
45487.09 |
4815 |
| M300634 |
213 |
3.122181 |
1.540972 |
Ileum |
B12 |
106635.900 |
42106.55 |
5384 |
| M300635 |
30 |
5.405679 |
2.215422 |
Ileum |
B12 |
NA |
NA |
NA |
| M300636 |
204 |
3.509144 |
1.743930 |
Ileum |
B12 |
106545.500 |
42220.70 |
5384 |
| M300637 |
51 |
2.910588 |
1.509677 |
Ileum |
B12 |
106948.100 |
42956.50 |
5384 |
| M300638 |
203 |
3.460643 |
1.642359 |
Ileum |
B12 |
106647.000 |
42288.86 |
5384 |
| M300639 |
224 |
2.990724 |
1.567194 |
Ileum |
B12 |
106800.500 |
41821.88 |
5384 |
| M300640 |
139 |
2.600750 |
1.476414 |
Ileum |
B12 |
107052.700 |
42525.49 |
5384 |
| M300641 |
98 |
27.021534 |
5.575144 |
Ileum |
B12 |
103203.400 |
38334.96 |
5384 |
| M300642 |
72 |
2.706444 |
1.584137 |
Ileum |
B12 |
108030.700 |
43599.50 |
4976 |
| M300643 |
16 |
5.123028 |
1.769523 |
Ileum |
B12 |
101876.900 |
39000.58 |
4976 |
| M300644 |
225 |
1.815382 |
1.244790 |
Ileum |
B12 |
NA |
NA |
NA |
| M300645 |
192 |
1.687109 |
1.278009 |
Ileum |
B12 |
107988.200 |
43509.47 |
4976 |
| M300646 |
64 |
13.841432 |
3.496467 |
Ileum |
B12 |
NA |
NA |
NA |
| M300647 |
201 |
3.557171 |
1.509236 |
Ileum |
B12 |
107969.500 |
43138.84 |
4976 |
| M300648 |
198 |
2.029309 |
1.315127 |
Ileum |
B12 |
107883.700 |
43169.50 |
4976 |
| M300649 |
74 |
4.148091 |
1.828161 |
Ileum |
B12 |
107984.200 |
43047.52 |
4976 |
| M300704 |
248 |
46.252453 |
4.111733 |
Colon |
B11 |
10676.967 |
15665.82 |
5140 |
| M300705 |
246 |
63.904552 |
3.974667 |
Colon |
B11 |
10812.315 |
15756.81 |
5140 |
| M300706 |
245 |
55.306851 |
4.105141 |
Colon |
B11 |
11055.416 |
15656.04 |
5140 |
| M300707 |
249 |
56.014561 |
4.107466 |
Colon |
B11 |
11216.842 |
15649.19 |
5140 |
| M300708 |
250 |
56.919155 |
3.968289 |
Colon |
B11 |
11879.874 |
15812.03 |
5140 |
| M300709 |
81 |
47.883513 |
4.609160 |
Colon |
B11 |
8479.772 |
19536.22 |
5140 |
| M300710 |
51 |
27.091373 |
4.608891 |
Colon |
B11 |
NA |
NA |
NA |
| M300711 |
251 |
55.676485 |
4.046441 |
Colon |
B11 |
12278.126 |
15716.47 |
5140 |
| M300712 |
251 |
58.724925 |
4.031074 |
Colon |
B11 |
12139.937 |
15889.85 |
4976 |
| M300713 |
21 |
14.819100 |
3.257271 |
Colon |
B11 |
8681.188 |
19729.90 |
4976 |
| M300714 |
249 |
54.478111 |
4.133304 |
Colon |
B11 |
12138.958 |
16135.22 |
4976 |
| M300715 |
251 |
57.788457 |
3.979188 |
Colon |
B11 |
12164.850 |
16944.14 |
4976 |
| M300716 |
249 |
60.671013 |
3.921632 |
Colon |
B11 |
12650.442 |
17948.63 |
4976 |
| M300717 |
249 |
59.400190 |
4.100718 |
Colon |
B11 |
13434.733 |
19286.92 |
4976 |
| M300718 |
250 |
59.781144 |
3.989150 |
Colon |
B11 |
13238.197 |
20246.16 |
4976 |
| M300719 |
64 |
9.437906 |
2.619712 |
Colon |
B11 |
NA |
NA |
NA |
| M300720 |
134 |
51.228630 |
4.251175 |
Colon |
B11 |
7385.375 |
20281.05 |
5306 |
| M300721 |
250 |
62.754999 |
3.906901 |
Colon |
B11 |
10372.825 |
20398.48 |
5306 |
| M300722 |
247 |
57.049492 |
4.044123 |
Colon |
B11 |
11173.110 |
20408.59 |
5306 |
| M300724 |
250 |
61.740250 |
4.007957 |
Colon |
B11 |
13295.246 |
18310.97 |
5306 |
| M300725 |
238 |
59.611724 |
3.747036 |
Colon |
B11 |
12939.033 |
18128.54 |
5306 |
| M300726 |
89 |
40.430701 |
5.493395 |
Colon |
B11 |
NA |
NA |
NA |
| M300727 |
251 |
58.839874 |
4.128478 |
Colon |
B11 |
12777.094 |
17606.38 |
5306 |
| M300728 |
97 |
56.384971 |
4.868447 |
Colon |
B11 |
NA |
NA |
NA |
| M300729 |
236 |
54.296016 |
3.909034 |
Colon |
B11 |
12551.788 |
21653.42 |
4815 |
| M300730 |
241 |
62.293446 |
4.038759 |
Colon |
B11 |
12478.733 |
21318.48 |
4815 |
| M300731 |
251 |
60.746384 |
3.722194 |
Colon |
B11 |
12362.879 |
20562.75 |
4815 |
| M300732 |
227 |
64.774842 |
4.057109 |
Colon |
B11 |
12575.296 |
20313.69 |
4815 |
| M300733 |
245 |
58.847813 |
3.927334 |
Colon |
B11 |
12653.670 |
19720.44 |
4815 |
| M300734 |
153 |
57.496349 |
3.636022 |
Colon |
B11 |
17189.272 |
29742.58 |
4815 |
| M300735 |
251 |
61.238385 |
3.925052 |
Colon |
B11 |
11471.313 |
19136.40 |
4815 |
| M300736 |
251 |
60.609377 |
3.980455 |
Colon |
B11 |
13507.345 |
18129.93 |
5647 |
| M300737 |
224 |
64.693351 |
3.988141 |
Colon |
B11 |
13457.119 |
17998.50 |
5647 |
| M300738 |
247 |
61.882156 |
3.928037 |
Colon |
B11 |
13010.058 |
17942.33 |
5647 |
| M300739 |
26 |
17.627844 |
4.247952 |
Colon |
B11 |
NA |
NA |
NA |
| M300740 |
123 |
55.283007 |
4.637859 |
Colon |
B11 |
17787.836 |
12522.88 |
5647 |
| M300741 |
250 |
58.936098 |
3.954625 |
Colon |
B11 |
12684.368 |
17716.75 |
5647 |
| M300742 |
251 |
59.273326 |
4.047533 |
Colon |
B11 |
12621.546 |
17543.54 |
5647 |
| M300743 |
250 |
60.307163 |
3.931065 |
Colon |
B11 |
12372.901 |
16657.60 |
5647 |
| M300744 |
245 |
61.953169 |
3.854428 |
Colon |
B11 |
11994.451 |
14153.13 |
4976 |
| M300745 |
251 |
60.978957 |
3.867243 |
Colon |
B11 |
12007.497 |
14299.24 |
4976 |
| M300746 |
46 |
10.208392 |
2.834892 |
Colon |
B11 |
NA |
NA |
NA |
| M300747 |
250 |
62.203433 |
3.804880 |
Colon |
B11 |
12029.348 |
14662.48 |
4976 |
| M300748 |
251 |
59.304676 |
3.841718 |
Colon |
B11 |
12076.591 |
15671.87 |
4976 |
| M300749 |
94 |
51.104739 |
4.166941 |
Colon |
B11 |
8706.301 |
29038.15 |
4976 |
| M300750 |
251 |
59.229995 |
3.963137 |
Colon |
B11 |
12060.510 |
16688.98 |
4976 |
| M300751 |
251 |
62.453455 |
3.921567 |
Colon |
B11 |
11931.196 |
19713.77 |
4976 |
| M300752 |
37 |
10.231365 |
3.454552 |
Colon |
B12 |
13243.970 |
30714.35 |
4815 |
| M300753 |
250 |
54.258825 |
3.870480 |
Colon |
B12 |
13884.299 |
20066.13 |
4815 |
| M300754 |
20 |
11.105970 |
3.441836 |
Colon |
B12 |
NA |
NA |
NA |
| M300755 |
250 |
56.033041 |
4.093147 |
Colon |
B12 |
13715.675 |
19528.97 |
4815 |
| M300756 |
250 |
53.959621 |
4.076681 |
Colon |
B12 |
13508.645 |
19087.25 |
4815 |
| M300757 |
251 |
54.271559 |
4.130368 |
Colon |
B12 |
13209.324 |
18911.46 |
4815 |
| M300758 |
251 |
60.601778 |
3.913348 |
Colon |
B12 |
13454.496 |
18211.88 |
4815 |
| M300759 |
252 |
57.034625 |
4.139033 |
Colon |
B12 |
13356.627 |
17525.29 |
4815 |
| M300760 |
249 |
52.510697 |
4.092732 |
Colon |
B12 |
12866.495 |
15050.07 |
5140 |
| M300761 |
251 |
55.107864 |
4.093000 |
Colon |
B12 |
12921.938 |
15311.99 |
5140 |
| M300762 |
28 |
8.726889 |
3.118462 |
Colon |
B12 |
NA |
NA |
NA |
| M300763 |
252 |
59.548863 |
4.016797 |
Colon |
B12 |
12995.946 |
15577.55 |
5140 |
| M300764 |
251 |
58.308107 |
3.910202 |
Colon |
B12 |
12999.107 |
16205.10 |
5140 |
| M300765 |
177 |
42.010405 |
4.149764 |
Colon |
B12 |
13266.800 |
30315.90 |
5140 |
| M300766 |
250 |
56.763364 |
4.133256 |
Colon |
B12 |
13128.597 |
18741.54 |
5140 |
| M300767 |
249 |
51.972455 |
4.006491 |
Colon |
B12 |
13103.684 |
20085.08 |
5140 |
| M300768 |
249 |
54.447298 |
4.031809 |
Colon |
B12 |
12299.778 |
15261.25 |
4815 |
| M300769 |
34 |
14.270606 |
3.890768 |
Colon |
B12 |
11581.666 |
28330.79 |
4815 |
| M300770 |
94 |
30.334103 |
4.919868 |
Colon |
B12 |
NA |
NA |
NA |
| M300771 |
248 |
57.969189 |
4.027783 |
Colon |
B12 |
12230.636 |
14216.24 |
4815 |
| M300772 |
250 |
59.731720 |
3.899035 |
Colon |
B12 |
12192.804 |
14393.52 |
4815 |
| M300773 |
252 |
62.413288 |
3.621678 |
Colon |
B12 |
12122.684 |
16011.33 |
4815 |
| M300774 |
251 |
56.385399 |
4.122407 |
Colon |
B12 |
12155.624 |
16716.47 |
4815 |
| M300775 |
250 |
53.553768 |
4.039717 |
Colon |
B12 |
12941.429 |
17792.21 |
4815 |
| M300776 |
251 |
57.024440 |
3.986191 |
Colon |
B12 |
10481.871 |
16446.70 |
5306 |
| M300777 |
215 |
63.829415 |
4.004581 |
Colon |
B12 |
10486.437 |
16559.54 |
5306 |
| M300778 |
250 |
57.359784 |
4.014746 |
Colon |
B12 |
10349.884 |
16974.87 |
5306 |
| M300779 |
19 |
10.646900 |
4.202734 |
Colon |
B12 |
NA |
NA |
NA |
| M300780 |
251 |
53.856346 |
4.031943 |
Colon |
B12 |
10386.112 |
17635.79 |
5306 |
| M300781 |
73 |
27.241929 |
4.346054 |
Colon |
B12 |
9381.647 |
30091.13 |
5306 |
| M300782 |
251 |
53.845025 |
4.039524 |
Colon |
B12 |
10499.609 |
18348.85 |
5306 |
| M300783 |
251 |
57.754394 |
4.054507 |
Colon |
B12 |
10505.179 |
19231.33 |
5306 |
| M300784 |
248 |
53.052589 |
4.019137 |
Colon |
B12 |
11637.205 |
19482.30 |
4656 |
| M300785 |
56 |
41.351511 |
4.731183 |
Colon |
B12 |
9262.832 |
30609.58 |
4656 |
| M300786 |
249 |
56.732741 |
4.172364 |
Colon |
B12 |
11099.177 |
18995.87 |
4656 |
| M300787 |
251 |
57.074180 |
4.060990 |
Colon |
B12 |
10460.974 |
19686.94 |
4656 |
| M300788 |
250 |
54.485767 |
4.019748 |
Colon |
B12 |
10442.084 |
20914.36 |
4656 |
| M300789 |
56 |
30.557213 |
4.776009 |
Colon |
B12 |
NA |
NA |
NA |
| M300790 |
155 |
39.641124 |
3.590062 |
Colon |
B12 |
10801.293 |
21241.46 |
4656 |
| M300791 |
249 |
49.310887 |
4.169707 |
Colon |
B12 |
11146.557 |
21763.22 |
4656 |
| M300792 |
251 |
55.663696 |
4.257795 |
Colon |
B12 |
11630.334 |
20543.59 |
5140 |
| M300793 |
152 |
30.393903 |
3.933883 |
Colon |
B12 |
NA |
NA |
NA |
| M300794 |
250 |
56.716658 |
4.055058 |
Colon |
B12 |
11673.937 |
21223.36 |
5140 |
| M300795 |
208 |
55.332481 |
3.811929 |
Colon |
B12 |
11602.686 |
22068.26 |
5140 |
| M300796 |
30 |
12.304417 |
4.442865 |
Colon |
B12 |
13661.804 |
28676.18 |
5140 |
| M300797 |
252 |
51.906800 |
4.046237 |
Colon |
B12 |
12879.975 |
20904.88 |
5140 |
| M300798 |
251 |
47.129111 |
4.133944 |
Colon |
B12 |
12256.492 |
21371.45 |
5140 |
| M300799 |
157 |
46.746231 |
3.709551 |
Colon |
B12 |
11843.311 |
19915.73 |
5140 |
# Print alpha diversity summary
alpha_diversity %>%
select(richness, neutral, phylogenetic, section, buffer) %>%
group_by(section, buffer) %>%
summarise(richness=mean(richness), neutral=mean(neutral), phylogenetic=mean(phylogenetic)) %>%
tt()
tinytable_5i3be4cibzi0xfjsaeul
| section |
buffer |
richness |
neutral |
phylogenetic |
| Caecum right |
B11 |
220.6250 |
50.239502 |
3.942011 |
| Caecum right |
B12 |
208.0833 |
46.973329 |
4.100613 |
| Colon |
B11 |
204.8085 |
53.573038 |
4.004198 |
| Colon |
B12 |
198.3750 |
46.906424 |
4.037582 |
| Ileum |
B11 |
137.4167 |
7.924440 |
2.229897 |
| Ileum |
B12 |
145.4583 |
6.016212 |
1.983800 |
alpha_diversity %>%
pivot_longer(!c(microsample,section,cryosection,type,buffer,batch,Xcoord,Ycoord,size), names_to = "metric", values_to = "value") %>%
left_join(quality,by=join_by(microsample==microsample)) %>%
mutate(metric=factor(metric,levels=c("richness","neutral","phylogenetic"))) %>%
ggplot(aes(x=section, y=value, color=quality, group=section))+
scale_color_gradient(low = "red", high = "green", name = "Quality") +
geom_boxplot(outlier.shape = NA) +
geom_jitter(width=0.2) +
facet_grid(metric ~ section, scales = "free")
